Metabolic diseases include obesity type 2 diabetes mellitus (insulin resistance) and non-alcoholic fatty liver disease (NAFLD). These disorders are associated with increased risk for cardiovascular diseases such as atherosclerosis and non-alcoholic steatohepatitis (NASH), and cancer. There is a marked increase in cancer risk of over 35% depending on the cancer type, associated with obesity, and insulin resistance. NAFLD and NASH are associated with markedly increased risk for liver cancer. A chronic imbalance between energy intake and energy expenditure causes obesity for which there is no safe and effective drug therapy. Accumulating reports indicate that hypoxia-inducible factors (HIFs), members of the basic helix-hoop-helix Per-Arnt-Sim (bHLH-PAS) transcription factor family, exert a pivotal role during the pathogenesis of NAFLD. HIF is a heterodimer of an oxygen-sensitive alpha subunit and a constitutively expressed beta subunit (HIF1beta or ARNT). Under normoxic conditions, HIFalpha (HIF1alpha and HIF2alpha) is rapidly hydroxylated and degraded by several prolyl hydroxylase domain enzymes (PHD) followed by conjugation with the von Hippel-Lindau (VHL) E3 ubiquitin ligase complex. Conversely, the HIF proteins are stabilized during hypoxia due to inhibition of PHD activity induced by low O2. Hepatocyte-specific disruption of PHD2 and PHD3 or VHL, which lead to overexpression of both HIF1alpha and HIF2alpha, was demonstrated to promote hepatic steatosis. Hepatic HIF2alpha but not HIF1alpha was further identified as a major regulator of hepatic lipid metabolism through the up-regulation of genes involved in fatty acid synthesis (Srebp1c (official symbol: Srebf1) and Fasn) and fatty acid uptake (Cd36) and the down-regulation of genes involved in regulating fatty acid beta-oxidation (Ppara and Acox1). Most studies on the relationship between HIF and NAFLD focused on evaluating the effects of liver HIF. However, liver HIF2alpha activation was recently observed to ameliorate hyperglycemia through the insulin-dependent pathway with increased insulin receptor substrate-2 (Irs2), or the insulin-independent pathway with the repression of glucagon action. These studies imply that pharmacological inhibition of liver HIF2alpha might not be suitable to exploit for NAFLD therapy, due to the increased risk of increased hepatic glucose production and type 2 diabetes. Several novel targets in the intestine were recently implicated in the development of NAFLD. While both HIF1alpha and HIF2alpha are expressed in the intestinal epithelial cells, the role of the intestine HIFalpha on the pathogenesis of NAFLD and other metabolic diseases is poorly understood. The intestine-specific knockout or activation of HIFalpha and metabolomics profiling analysis were adopted to clarify the role and dissect the precise mechanism of intestine HIFalpha in NAFLD development. This study revealed that intestine HIF2alpha but not HIF1alpha signaling is activated during obesity. Intestine-specific Hif2a (official symbol: Epas1) ablation substantially ameliorates high-fat diet (HFD)-induced obesity and hepatic steatosis in mice. Amelioration of the adverse metabolic phenotypes is correlated with alterations in ceramide metabolism. Neu3, encoding a key enzyme in the ceramide salvage pathway, was identified as a novel target gene of HIF2alpha. A HIF2alpha-NEU3-ceramide axis was found to influence NAFLD development. Notably, a specific HIF2alpha inhibitor PT2385, which is in clinical trials for the treatment of renal cancer, was found to prevent and reverse metabolic disorders through the inhibition of intestinal HIF2alpha. This work suggests that intestine HIF2alpha is a novel target for the treatment of NAFLD. Human intestine biopsies from individuals with or without obesity revealed a relationship between activated HIF2alpha but not HIF1alpha in higher body mass index and hepatic toxicity. The causality of this correlation was verified in mice with an intestine-specific Hif2a-disruption, in which high-fat diet-induced hepatic steatosis and obesity were substantially lower. PT2385, a HIF2alpha -specific inhibitor, had preventive and therapeutic effects on metabolic disorders dependent on intestine HIF2 alpha. Intestine HIF2alpha inhibition markedly reduced intestine and serum ceramide levels. Mechanistically, intestine HIF2 alpha regulates ceramide metabolism mainly from the salvage pathway, revealed by the identification of the novel HIF2alpha target gene encoding neuraminidase 3. These results suggest that intestine HIF2alpha would be a viable target for hepatic steatosis therapy. Recently, intermittent fasting was demonstrated to optimize energy metabolism and promote health primarily through weight loss. However, the mechanism for these benefits is unclear. Notably, one study found that time-restricted feeding can counteract obesity without reducing energy intake. Although the perturbation of circadian rhythm was considered as a significant contributor to the increased energy expenditure, the possibility exists that the white adipose browning would be a more direct mechanism. Therefore, in the current study, mice were placed on an every-other-day fasting (EODF) regimen to explore the effect on white adipose beiging and metabolic disorders. Evidence suggests that EODF selectively activates beige thermogenesis and ameliorates obesity-related metabolic diseases probably via the microbiota-beige fat axis. While activation of beige thermogenesis is a promising approach for treatment of obesity-associated diseases, there are currently no known pharmacological means to induce beiging in humans. Intermittent fasting is an effective and natural strategy for weight control, but the mechanism for its efficacy is poorly understood. Here, we show that the EODF regimen selectively stimulates beige fat development within white adipose tissue, and dramatically ameliorates obesity, insulin resistance and hepatic steatosis. EODF treatment results in a shift in the gut microbiota composition leading to the elevation of the fermentation products acetate and lactate, and the selective upregulation of monocarboxylate transporter 1 expression in beige cells. Microbiota-depleted mice are resistance to EODF-induced beiging, while transplantation of the microbiota from EODF-treated mice to microbiota-depleted mice activates beiging and improves metabolic homeostasis. These findings provide a new gut microbiota-driven mechanism for activating adipose tissue browning and treating metabolic diseases.